noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.4.1.3.2.1.21) Plots of Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.4.1.3.2.1.21.2) Iterating over all combinations of grouping variables
(1.4.1.3.2.1.21.2.1) Entire pool of samples
(1.4.1.3.2.1.21.2.2) Iterating over Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order
(1.4.1.3.2.1.21.2.2.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order: GeneSelector paired test ranking
(1.4.1.3.2.1.21.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.4.1.3.2.1.21.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.4.1.3.2.1.21.2.2.2.1.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.3.2.1.21.2.2.2.1.1.0) Table 240. Data table used for plots. Data for all pooled samples. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.2.1.21.2.2.2.1.1.0-3234b0dcd1e.1.4.1.3.2.1.21.2.2.csv

.record.id feature l2fc
SB11.before.diet N_0 -0.0076750
SB16.before.diet N_0 0.3480865
SB18.before.diet N_0 -0.5212565
SB28.before.diet N_0 -0.2328718
SB29.before.diet N_0 1.6539099
SB34.before.diet N_0 0.1571710
SB36.before.diet N_0 -0.3610002
SB39.before.diet N_0 0.5340419
SB4.before.diet N_0 0.8992148
SB41.before.diet N_0 -0.2760230
SB43.before.diet N_0 -0.0482601
SB44.before.diet N_0 -0.2396756
SB5.before.diet N_0 0.6115110
SB9.before.diet N_0 0.5547278
SB11.before.diet N_0.25 -0.0650435
SB16.before.diet N_0.25 0.4305600
SB18.before.diet N_0.25 -1.0194469
SB28.before.diet N_0.25 -0.4169106
SB29.before.diet N_0.25 1.6552423
SB34.before.diet N_0.25 0.2272344
SB36.before.diet N_0.25 -0.3358437
SB39.before.diet N_0.25 0.6966606
SB4.before.diet N_0.25 1.2180988
SB41.before.diet N_0.25 -0.2694241
SB43.before.diet N_0.25 -0.1440967
SB44.before.diet N_0.25 -0.4737334
SB5.before.diet N_0.25 0.8732202
SB9.before.diet N_0.25 0.7805925
SB11.before.diet N_0.5 -0.1685488
SB16.before.diet N_0.5 0.3546864
SB18.before.diet N_0.5 -1.5752688
SB28.before.diet N_0.5 -0.3743272
SB29.before.diet N_0.5 1.1220989
SB34.before.diet N_0.5 0.2693997
SB36.before.diet N_0.5 -0.2064812
SB39.before.diet N_0.5 0.8565193
SB4.before.diet N_0.5 1.1867101
SB41.before.diet N_0.5 -0.2279777
SB43.before.diet N_0.5 -0.3132971
SB44.before.diet N_0.5 -0.8638242
SB5.before.diet N_0.5 1.2256564
SB9.before.diet N_0.5 1.0160234
SB11.before.diet N_1 -0.3772457
SB16.before.diet N_1 -0.1316451
SB18.before.diet N_1 -2.0354925
SB28.before.diet N_1 0.1598985
SB29.before.diet N_1 0.0459187
SB34.before.diet N_1 0.1933201
SB36.before.diet N_1 0.0025508
SB39.before.diet N_1 0.9765652
SB4.before.diet N_1 0.4759275
SB41.before.diet N_1 -0.0979754
SB43.before.diet N_1 -0.6827017
SB44.before.diet N_1 -1.5533243
SB5.before.diet N_1 1.8463379
SB9.before.diet N_1 1.3145478
SB11.before.diet N_2 -0.3304349
SB16.before.diet N_2 -0.3551647
SB18.before.diet N_2 -1.8716221
SB28.before.diet N_2 0.6421860
SB29.before.diet N_2 -0.3746549
SB34.before.diet N_2 0.0780092
SB36.before.diet N_2 -0.0577498
SB39.before.diet N_2 0.8045594
SB4.before.diet N_2 0.1615020
SB41.before.diet N_2 -0.0316386
SB43.before.diet N_2 -0.9722183
SB44.before.diet N_2 -1.7133320
SB5.before.diet N_2 2.1562494
SB9.before.diet N_2 1.2631519
SB11.before.diet N_4 -0.1400163
SB16.before.diet N_4 -0.2930996
SB18.before.diet N_4 -1.6096349
SB28.before.diet N_4 0.6192234
SB29.before.diet N_4 -0.3728553
SB34.before.diet N_4 0.0519709
SB36.before.diet N_4 -0.2104588
SB39.before.diet N_4 0.6384434
SB4.before.diet N_4 0.1080544
SB41.before.diet N_4 -0.0205202
SB43.before.diet N_4 -1.0084253
SB44.before.diet N_4 -1.5371088
SB5.before.diet N_4 2.0475122
SB9.before.diet N_4 1.0190013
SB11.before.diet N_8 -0.0844503
SB16.before.diet N_8 -0.2526492
SB18.before.diet N_8 -1.4361547
SB28.before.diet N_8 0.5420799
SB29.before.diet N_8 -0.3292086
SB34.before.diet N_8 0.0445451
SB36.before.diet N_8 -0.2583259
SB39.before.diet N_8 0.5531758
SB4.before.diet N_8 0.0926171
SB41.before.diet N_8 -0.0175829
SB43.before.diet N_8 -0.9373780
SB44.before.diet N_8 -1.3823433
SB5.before.diet N_8 1.8661135
SB9.before.diet N_8 0.8830117
SB11.before.diet N_Inf -0.0716940
SB16.before.diet N_Inf -0.2210522
SB18.before.diet N_Inf -1.2604795
SB28.before.diet N_Inf 0.4743894
SB29.before.diet N_Inf -0.2881601
SB34.before.diet N_Inf 0.0389764
SB36.before.diet N_Inf -0.2389022
SB39.before.diet N_Inf 0.4840702
SB4.before.diet N_Inf 0.0810394
SB41.before.diet N_Inf -0.0153837
SB43.before.diet N_Inf -0.8233896
SB44.before.diet N_Inf -1.2138795
SB5.before.diet N_Inf 1.6399664
SB9.before.diet N_Inf 0.7727269
SB11.before.diet NE_0.25 -0.0580629
SB16.before.diet NE_0.25 0.0804739
SB18.before.diet NE_0.25 -0.4968010
SB28.before.diet NE_0.25 -0.1834798
SB29.before.diet NE_0.25 -0.0034139
SB34.before.diet NE_0.25 0.0681398
SB36.before.diet NE_0.25 0.0213113
SB39.before.diet NE_0.25 0.1559748
SB4.before.diet NE_0.25 0.3118199
SB41.before.diet NE_0.25 0.0074359
SB43.before.diet NE_0.25 -0.0947365
SB44.before.diet NE_0.25 -0.2334653
SB5.before.diet NE_0.25 0.2564894
SB9.before.diet NE_0.25 0.2198809
SB11.before.diet NE_0.5 -0.1623359
SB16.before.diet NE_0.5 0.0004776
SB18.before.diet NE_0.5 -1.0480772
SB28.before.diet NE_0.5 -0.1402940
SB29.before.diet NE_0.5 -0.5402037
SB34.before.diet NE_0.5 0.1085280
SB36.before.diet NE_0.5 0.1476659
SB39.before.diet NE_0.5 0.3079463
SB4.before.diet NE_0.5 0.2676527
SB41.before.diet NE_0.5 0.0500777
SB43.before.diet NE_0.5 -0.2634219
SB44.before.diet NE_0.5 -0.6230980
SB5.before.diet NE_0.5 0.6041029
SB9.before.diet NE_0.5 0.4500457
SB11.before.diet NE_1 -0.3722349
SB16.before.diet NE_1 -0.4904583
SB18.before.diet NE_1 -1.4992576
SB28.before.diet NE_1 0.3944830
SB29.before.diet NE_1 -1.6181548
SB34.before.diet NE_1 0.0334600
SB36.before.diet NE_1 0.3550983
SB39.before.diet NE_1 0.4172732
SB4.before.diet NE_1 -0.4519847
SB41.before.diet NE_1 0.1797185
SB43.before.diet NE_1 -0.6330088
SB44.before.diet NE_1 -1.3126390
SB5.before.diet NE_1 1.2215903
SB9.before.diet NE_1 0.7449994
SB11.before.diet NE_2 -0.3263374
SB16.before.diet NE_2 -0.7138983
SB18.before.diet NE_2 -1.3316416
SB28.before.diet NE_2 0.8771701
SB29.before.diet NE_2 -2.0387634
SB34.before.diet NE_2 -0.0769682
SB36.before.diet NE_2 0.2946857
SB39.before.diet NE_2 0.2439923
SB4.before.diet NE_2 -0.7675982
SB41.before.diet NE_2 0.2445872
SB43.before.diet NE_2 -0.9240809
SB44.before.diet NE_2 -1.4717210
SB5.before.diet NE_2 1.5327491
SB9.before.diet NE_2 0.6951462
SB11.before.diet NE_4 -0.1358420
SB16.before.diet NE_4 -0.6515895
SB18.before.diet NE_4 -1.0686691
SB28.before.diet NE_4 0.8542210
SB29.before.diet NE_4 -2.0369209
SB34.before.diet NE_4 -0.1011699
SB36.before.diet NE_4 0.1414095
SB39.before.diet NE_4 0.0793540
SB4.before.diet NE_4 -0.8212649
SB41.before.diet NE_4 0.2552103
SB43.before.diet NE_4 -0.9628342
SB44.before.diet NE_4 -1.2940856
SB5.before.diet NE_4 1.4240996
SB9.before.diet NE_4 0.4516693
SB11.before.diet NE_8 -0.0800269
SB16.before.diet NE_8 -0.6110654
SB18.before.diet NE_8 -0.8948597
SB28.before.diet NE_8 0.7770790
SB29.before.diet NE_8 -1.9931985
SB34.before.diet NE_8 -0.1080232
SB36.before.diet NE_8 0.0933700
SB39.before.diet NE_8 -0.0053785
SB4.before.diet NE_8 -0.8367663
SB41.before.diet NE_8 0.2579894
SB43.before.diet NE_8 -0.8936277
SB44.before.diet NE_8 -1.1388512
SB5.before.diet NE_8 1.2420011
SB9.before.diet NE_8 0.3157548
SB11.before.diet NE_Inf -0.0672732
SB16.before.diet NE_Inf -0.5794113
SB18.before.diet NE_Inf -0.7189372
SB28.before.diet NE_Inf 0.7093968

(1.4.1.3.2.1.21.2.2.2.1.1.1) Widget 254. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data for all pooled samples. Click to see HTML widget file in full window: ./1.4.1.3.2.1.21.2.2.2.1.1.1-3237cb92772Dynamic.Pivot.Table.html

(1.4.1.3.2.1.21.2.2.2.1.1.1) Widget 255. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data for all pooled samples. Click to see HTML widget file in full window: ./1.4.1.3.2.1.21.2.2.2.1.1.1-32372769ea1Dynamic.Pivot.Table.html

(1.4.1.3.2.1.21.2.2.2.1.1.1) Table 241. Summary table. Data for all pooled samples. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.2.1.21.2.2.2.1.1.1-3231826019e.1.4.1.3.2.1.21.2.2.csv

feature mean sd median incidence
N_0 0.219421 0.5932 0.07475 0.5000
N_0.25 0.225508 0.7470 0.08110 0.5000
N_0.5 0.164384 0.8478 0.05043 0.5000
NE_8 -0.276829 0.8417 -0.09403 0.3571
NE_Inf -0.271447 0.7636 -0.09363 0.3571
N_1 0.009763 1.0218 0.02423 0.5714
NE_4 -0.276172 0.9201 -0.11851 0.4286
N_4 -0.050565 0.9711 -0.08027 0.4286
NE_2 -0.268763 0.9984 -0.20165 0.4286
N_8 -0.051182 0.8742 -0.05102 0.4286
N_2 -0.042940 1.0768 -0.04469 0.4286
N_Inf -0.045841 0.7676 -0.04354 0.4286
NE_0.5 -0.060067 0.4484 0.02528 0.5714
NE_0.25 0.003683 0.2138 0.01437 0.5714
NE_1 -0.216508 0.8528 -0.16939 0.5000

(1.4.1.3.2.1.21.2.2.2.1.1.1) Figure 748. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar_stacked plot. Image file: plots/323322ac685.svg.

(1.4.1.3.2.1.21.2.2.2.1.1.1) Figure 749. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3233a2a03e4.svg.

(1.4.1.3.2.1.21.2.2.2.1.1.1) Figure 750. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3234c661a0e.svg.

(1.4.1.3.2.1.21.2.2.2.1.1.1) Figure 751. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3237524c692.svg.

(1.4.1.3.2.1.21.2.2.2.1.2) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.3.2.1.21.2.2.2.1.2.1) Figure 752. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3232c350105.svg.

(1.4.1.3.2.1.21.2.2.2.1.2.1) Figure 753. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3234d6d1368.svg.

(1.4.1.3.2.1.21.2.2.2.1.2.1) Figure 754. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3237d0fb5e3.svg.

(1.4.1.3.2.1.21.2.3) Grouping variables Drug.Before.Diet
(1.4.1.3.2.1.21.2.4) Iterating over Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order
(1.4.1.3.2.1.21.2.4.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order: GeneSelector paired test ranking
(1.4.1.3.2.1.21.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.4.1.3.2.1.21.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.4.1.3.2.1.21.2.4.2.1.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.3.2.1.21.2.4.2.1.1.0) Table 242. Data table used for plots. Data grouped by Drug.Before.Diet. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.2.1.21.2.4.2.1.1.0-3231ffd5120.1.4.1.3.2.1.21.2.4.csv

.record.id Drug.Before.Diet feature l2fc
SB11.before.diet DrugBefore_NO N_0 -0.0076750
SB16.before.diet DrugBefore_YES N_0 0.3480865
SB18.before.diet DrugBefore_NO N_0 -0.5212565
SB28.before.diet DrugBefore_YES N_0 -0.2328718
SB29.before.diet DrugBefore_YES N_0 1.6539099
SB34.before.diet DrugBefore_YES N_0 0.1571710
SB36.before.diet DrugBefore_YES N_0 -0.3610002
SB39.before.diet DrugBefore_YES N_0 0.5340419
SB4.before.diet DrugBefore_YES N_0 0.8992148
SB41.before.diet DrugBefore_YES N_0 -0.2760230
SB43.before.diet DrugBefore_YES N_0 -0.0482601
SB44.before.diet DrugBefore_YES N_0 -0.2396756
SB5.before.diet DrugBefore_NO N_0 0.6115110
SB9.before.diet DrugBefore_NO N_0 0.5547278
SB11.before.diet DrugBefore_NO N_0.25 -0.0650435
SB16.before.diet DrugBefore_YES N_0.25 0.4305600
SB18.before.diet DrugBefore_NO N_0.25 -1.0194469
SB28.before.diet DrugBefore_YES N_0.25 -0.4169106
SB29.before.diet DrugBefore_YES N_0.25 1.6552423
SB34.before.diet DrugBefore_YES N_0.25 0.2272344
SB36.before.diet DrugBefore_YES N_0.25 -0.3358437
SB39.before.diet DrugBefore_YES N_0.25 0.6966606
SB4.before.diet DrugBefore_YES N_0.25 1.2180988
SB41.before.diet DrugBefore_YES N_0.25 -0.2694241
SB43.before.diet DrugBefore_YES N_0.25 -0.1440967
SB44.before.diet DrugBefore_YES N_0.25 -0.4737334
SB5.before.diet DrugBefore_NO N_0.25 0.8732202
SB9.before.diet DrugBefore_NO N_0.25 0.7805925
SB11.before.diet DrugBefore_NO N_0.5 -0.1685488
SB16.before.diet DrugBefore_YES N_0.5 0.3546864
SB18.before.diet DrugBefore_NO N_0.5 -1.5752688
SB28.before.diet DrugBefore_YES N_0.5 -0.3743272
SB29.before.diet DrugBefore_YES N_0.5 1.1220989
SB34.before.diet DrugBefore_YES N_0.5 0.2693997
SB36.before.diet DrugBefore_YES N_0.5 -0.2064812
SB39.before.diet DrugBefore_YES N_0.5 0.8565193
SB4.before.diet DrugBefore_YES N_0.5 1.1867101
SB41.before.diet DrugBefore_YES N_0.5 -0.2279777
SB43.before.diet DrugBefore_YES N_0.5 -0.3132971
SB44.before.diet DrugBefore_YES N_0.5 -0.8638242
SB5.before.diet DrugBefore_NO N_0.5 1.2256564
SB9.before.diet DrugBefore_NO N_0.5 1.0160234
SB11.before.diet DrugBefore_NO N_1 -0.3772457
SB16.before.diet DrugBefore_YES N_1 -0.1316451
SB18.before.diet DrugBefore_NO N_1 -2.0354925
SB28.before.diet DrugBefore_YES N_1 0.1598985
SB29.before.diet DrugBefore_YES N_1 0.0459187
SB34.before.diet DrugBefore_YES N_1 0.1933201
SB36.before.diet DrugBefore_YES N_1 0.0025508
SB39.before.diet DrugBefore_YES N_1 0.9765652
SB4.before.diet DrugBefore_YES N_1 0.4759275
SB41.before.diet DrugBefore_YES N_1 -0.0979754
SB43.before.diet DrugBefore_YES N_1 -0.6827017
SB44.before.diet DrugBefore_YES N_1 -1.5533243
SB5.before.diet DrugBefore_NO N_1 1.8463379
SB9.before.diet DrugBefore_NO N_1 1.3145478
SB11.before.diet DrugBefore_NO N_2 -0.3304349
SB16.before.diet DrugBefore_YES N_2 -0.3551647
SB18.before.diet DrugBefore_NO N_2 -1.8716221
SB28.before.diet DrugBefore_YES N_2 0.6421860
SB29.before.diet DrugBefore_YES N_2 -0.3746549
SB34.before.diet DrugBefore_YES N_2 0.0780092
SB36.before.diet DrugBefore_YES N_2 -0.0577498
SB39.before.diet DrugBefore_YES N_2 0.8045594
SB4.before.diet DrugBefore_YES N_2 0.1615020
SB41.before.diet DrugBefore_YES N_2 -0.0316386
SB43.before.diet DrugBefore_YES N_2 -0.9722183
SB44.before.diet DrugBefore_YES N_2 -1.7133320
SB5.before.diet DrugBefore_NO N_2 2.1562494
SB9.before.diet DrugBefore_NO N_2 1.2631519
SB11.before.diet DrugBefore_NO N_4 -0.1400163
SB16.before.diet DrugBefore_YES N_4 -0.2930996
SB18.before.diet DrugBefore_NO N_4 -1.6096349
SB28.before.diet DrugBefore_YES N_4 0.6192234
SB29.before.diet DrugBefore_YES N_4 -0.3728553
SB34.before.diet DrugBefore_YES N_4 0.0519709
SB36.before.diet DrugBefore_YES N_4 -0.2104588
SB39.before.diet DrugBefore_YES N_4 0.6384434
SB4.before.diet DrugBefore_YES N_4 0.1080544
SB41.before.diet DrugBefore_YES N_4 -0.0205202
SB43.before.diet DrugBefore_YES N_4 -1.0084253
SB44.before.diet DrugBefore_YES N_4 -1.5371088
SB5.before.diet DrugBefore_NO N_4 2.0475122
SB9.before.diet DrugBefore_NO N_4 1.0190013
SB11.before.diet DrugBefore_NO N_8 -0.0844503
SB16.before.diet DrugBefore_YES N_8 -0.2526492
SB18.before.diet DrugBefore_NO N_8 -1.4361547
SB28.before.diet DrugBefore_YES N_8 0.5420799
SB29.before.diet DrugBefore_YES N_8 -0.3292086
SB34.before.diet DrugBefore_YES N_8 0.0445451
SB36.before.diet DrugBefore_YES N_8 -0.2583259
SB39.before.diet DrugBefore_YES N_8 0.5531758
SB4.before.diet DrugBefore_YES N_8 0.0926171
SB41.before.diet DrugBefore_YES N_8 -0.0175829
SB43.before.diet DrugBefore_YES N_8 -0.9373780
SB44.before.diet DrugBefore_YES N_8 -1.3823433
SB5.before.diet DrugBefore_NO N_8 1.8661135
SB9.before.diet DrugBefore_NO N_8 0.8830117
SB11.before.diet DrugBefore_NO N_Inf -0.0716940
SB16.before.diet DrugBefore_YES N_Inf -0.2210522
SB18.before.diet DrugBefore_NO N_Inf -1.2604795
SB28.before.diet DrugBefore_YES N_Inf 0.4743894
SB29.before.diet DrugBefore_YES N_Inf -0.2881601
SB34.before.diet DrugBefore_YES N_Inf 0.0389764
SB36.before.diet DrugBefore_YES N_Inf -0.2389022
SB39.before.diet DrugBefore_YES N_Inf 0.4840702
SB4.before.diet DrugBefore_YES N_Inf 0.0810394
SB41.before.diet DrugBefore_YES N_Inf -0.0153837
SB43.before.diet DrugBefore_YES N_Inf -0.8233896
SB44.before.diet DrugBefore_YES N_Inf -1.2138795
SB5.before.diet DrugBefore_NO N_Inf 1.6399664
SB9.before.diet DrugBefore_NO N_Inf 0.7727269
SB11.before.diet DrugBefore_NO NE_0.25 -0.0580629
SB16.before.diet DrugBefore_YES NE_0.25 0.0804739
SB18.before.diet DrugBefore_NO NE_0.25 -0.4968010
SB28.before.diet DrugBefore_YES NE_0.25 -0.1834798
SB29.before.diet DrugBefore_YES NE_0.25 -0.0034139
SB34.before.diet DrugBefore_YES NE_0.25 0.0681398
SB36.before.diet DrugBefore_YES NE_0.25 0.0213113
SB39.before.diet DrugBefore_YES NE_0.25 0.1559748
SB4.before.diet DrugBefore_YES NE_0.25 0.3118199
SB41.before.diet DrugBefore_YES NE_0.25 0.0074359
SB43.before.diet DrugBefore_YES NE_0.25 -0.0947365
SB44.before.diet DrugBefore_YES NE_0.25 -0.2334653
SB5.before.diet DrugBefore_NO NE_0.25 0.2564894
SB9.before.diet DrugBefore_NO NE_0.25 0.2198809
SB11.before.diet DrugBefore_NO NE_0.5 -0.1623359
SB16.before.diet DrugBefore_YES NE_0.5 0.0004776
SB18.before.diet DrugBefore_NO NE_0.5 -1.0480772
SB28.before.diet DrugBefore_YES NE_0.5 -0.1402940
SB29.before.diet DrugBefore_YES NE_0.5 -0.5402037
SB34.before.diet DrugBefore_YES NE_0.5 0.1085280
SB36.before.diet DrugBefore_YES NE_0.5 0.1476659
SB39.before.diet DrugBefore_YES NE_0.5 0.3079463
SB4.before.diet DrugBefore_YES NE_0.5 0.2676527
SB41.before.diet DrugBefore_YES NE_0.5 0.0500777
SB43.before.diet DrugBefore_YES NE_0.5 -0.2634219
SB44.before.diet DrugBefore_YES NE_0.5 -0.6230980
SB5.before.diet DrugBefore_NO NE_0.5 0.6041029
SB9.before.diet DrugBefore_NO NE_0.5 0.4500457
SB11.before.diet DrugBefore_NO NE_1 -0.3722349
SB16.before.diet DrugBefore_YES NE_1 -0.4904583
SB18.before.diet DrugBefore_NO NE_1 -1.4992576
SB28.before.diet DrugBefore_YES NE_1 0.3944830
SB29.before.diet DrugBefore_YES NE_1 -1.6181548
SB34.before.diet DrugBefore_YES NE_1 0.0334600
SB36.before.diet DrugBefore_YES NE_1 0.3550983
SB39.before.diet DrugBefore_YES NE_1 0.4172732
SB4.before.diet DrugBefore_YES NE_1 -0.4519847
SB41.before.diet DrugBefore_YES NE_1 0.1797185
SB43.before.diet DrugBefore_YES NE_1 -0.6330088
SB44.before.diet DrugBefore_YES NE_1 -1.3126390
SB5.before.diet DrugBefore_NO NE_1 1.2215903
SB9.before.diet DrugBefore_NO NE_1 0.7449994
SB11.before.diet DrugBefore_NO NE_2 -0.3263374
SB16.before.diet DrugBefore_YES NE_2 -0.7138983
SB18.before.diet DrugBefore_NO NE_2 -1.3316416
SB28.before.diet DrugBefore_YES NE_2 0.8771701
SB29.before.diet DrugBefore_YES NE_2 -2.0387634
SB34.before.diet DrugBefore_YES NE_2 -0.0769682
SB36.before.diet DrugBefore_YES NE_2 0.2946857
SB39.before.diet DrugBefore_YES NE_2 0.2439923
SB4.before.diet DrugBefore_YES NE_2 -0.7675982
SB41.before.diet DrugBefore_YES NE_2 0.2445872
SB43.before.diet DrugBefore_YES NE_2 -0.9240809
SB44.before.diet DrugBefore_YES NE_2 -1.4717210
SB5.before.diet DrugBefore_NO NE_2 1.5327491
SB9.before.diet DrugBefore_NO NE_2 0.6951462
SB11.before.diet DrugBefore_NO NE_4 -0.1358420
SB16.before.diet DrugBefore_YES NE_4 -0.6515895
SB18.before.diet DrugBefore_NO NE_4 -1.0686691
SB28.before.diet DrugBefore_YES NE_4 0.8542210
SB29.before.diet DrugBefore_YES NE_4 -2.0369209
SB34.before.diet DrugBefore_YES NE_4 -0.1011699
SB36.before.diet DrugBefore_YES NE_4 0.1414095
SB39.before.diet DrugBefore_YES NE_4 0.0793540
SB4.before.diet DrugBefore_YES NE_4 -0.8212649
SB41.before.diet DrugBefore_YES NE_4 0.2552103
SB43.before.diet DrugBefore_YES NE_4 -0.9628342
SB44.before.diet DrugBefore_YES NE_4 -1.2940856
SB5.before.diet DrugBefore_NO NE_4 1.4240996
SB9.before.diet DrugBefore_NO NE_4 0.4516693
SB11.before.diet DrugBefore_NO NE_8 -0.0800269
SB16.before.diet DrugBefore_YES NE_8 -0.6110654
SB18.before.diet DrugBefore_NO NE_8 -0.8948597
SB28.before.diet DrugBefore_YES NE_8 0.7770790
SB29.before.diet DrugBefore_YES NE_8 -1.9931985
SB34.before.diet DrugBefore_YES NE_8 -0.1080232
SB36.before.diet DrugBefore_YES NE_8 0.0933700
SB39.before.diet DrugBefore_YES NE_8 -0.0053785
SB4.before.diet DrugBefore_YES NE_8 -0.8367663
SB41.before.diet DrugBefore_YES NE_8 0.2579894
SB43.before.diet DrugBefore_YES NE_8 -0.8936277
SB44.before.diet DrugBefore_YES NE_8 -1.1388512
SB5.before.diet DrugBefore_NO NE_8 1.2420011
SB9.before.diet DrugBefore_NO NE_8 0.3157548
SB11.before.diet DrugBefore_NO NE_Inf -0.0672732
SB16.before.diet DrugBefore_YES NE_Inf -0.5794113
SB18.before.diet DrugBefore_NO NE_Inf -0.7189372
SB28.before.diet DrugBefore_YES NE_Inf 0.7093968

(1.4.1.3.2.1.21.2.4.2.1.1.1) Widget 256. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet. Click to see HTML widget file in full window: ./1.4.1.3.2.1.21.2.4.2.1.1.1-3234a05dd45Dynamic.Pivot.Table.html

(1.4.1.3.2.1.21.2.4.2.1.1.1) Widget 257. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet. Click to see HTML widget file in full window: ./1.4.1.3.2.1.21.2.4.2.1.1.1-32377ea26f9Dynamic.Pivot.Table.html

(1.4.1.3.2.1.21.2.4.2.1.1.1) Table 243. Summary table. Data grouped by Drug.Before.Diet. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.2.1.21.2.4.2.1.1.1-3236342aeb7.1.4.1.3.2.1.21.2.4.csv

feature Drug.Before.Diet mean sd median incidence
N_0 DrugBefore_NO 0.15933 0.5329 0.27353 0.5
N_0 DrugBefore_YES 0.24346 0.6414 0.05446 0.5
N_0.25 DrugBefore_NO 0.14233 0.8821 0.35777 0.5
N_0.25 DrugBefore_YES 0.25878 0.7364 0.04157 0.5
N_0.5 DrugBefore_NO 0.12447 1.2887 0.42374 0.5
N_0.5 DrugBefore_YES 0.18035 0.6955 0.03146 0.5
NE_8 DrugBefore_NO 0.14572 0.8878 0.11786 0.5
NE_8 DrugBefore_YES -0.44585 0.8059 -0.35954 0.3
NE_Inf DrugBefore_NO 0.10865 0.7182 0.06911 0.5
NE_Inf DrugBefore_YES -0.42349 0.7619 -0.34629 0.3
N_1 DrugBefore_NO 0.18704 1.7590 0.46865 0.5
N_1 DrugBefore_YES -0.06115 0.6761 0.02423 0.6
NE_4 DrugBefore_NO 0.16781 1.0456 0.15791 0.5
NE_4 DrugBefore_YES -0.45377 0.8578 -0.37638 0.4
N_4 DrugBefore_NO 0.32922 1.5714 0.43949 0.5
N_4 DrugBefore_YES -0.20248 0.6704 -0.11549 0.4
NE_2 DrugBefore_NO 0.14248 1.2425 0.18440 0.5
NE_2 DrugBefore_YES -0.43326 0.9055 -0.39543 0.4
N_8 DrugBefore_NO 0.30713 1.4088 0.39928 0.5
N_8 DrugBefore_YES -0.19451 0.6019 -0.13512 0.4
N_2 DrugBefore_NO 0.30434 1.7783 0.46636 0.5
N_2 DrugBefore_YES -0.18185 0.7388 -0.04469 0.4
N_Inf DrugBefore_NO 0.27013 1.2368 0.35052 0.5
N_Inf DrugBefore_YES -0.17223 0.5283 -0.11822 0.4
NE_0.5 DrugBefore_NO -0.03907 0.7497 0.14385 0.5
NE_0.5 DrugBefore_YES -0.06847 0.3206 0.02528 0.6
NE_0.25 DrugBefore_NO -0.01962 0.3477 0.08091 0.5
NE_0.25 DrugBefore_YES 0.01301 0.1594 0.01437 0.6
NE_1 DrugBefore_NO 0.02377 1.2154 0.18638 0.5
NE_1 DrugBefore_YES -0.31262 0.7226 -0.20926 0.5

(1.4.1.3.2.1.21.2.4.2.1.1.1) Figure 755. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar_stacked plot. Image file: plots/32316e26e0b.svg.

(1.4.1.3.2.1.21.2.4.2.1.1.1) Figure 756. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3235d9f7e7d.svg.

(1.4.1.3.2.1.21.2.4.2.1.1.1) Figure 757. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3231794236f.svg.

(1.4.1.3.2.1.21.2.4.2.1.1.1) Figure 758. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/32377c7e97e.svg.

(1.4.1.3.2.1.21.2.4.2.1.2) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.3.2.1.21.2.4.2.1.2.1) Figure 759. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3237e2b2e21.svg.

(1.4.1.3.2.1.21.2.4.2.1.2.1) Figure 760. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3236bcb0761.svg.

(1.4.1.3.2.1.21.2.4.2.1.2.1) Figure 761. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3238ff860e.svg.

(1.4.1.3.2.1.21.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.4.1.3.2.1.21.2.4.2.2.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.3.2.1.21.2.4.2.2.1.1) Figure 762. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3232dafd815.svg.

(1.4.1.3.2.1.21.2.4.2.2.1.1) Figure 763. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3233ba3768a.svg.

(1.4.1.3.2.1.21.2.4.2.2.1.1) Figure 764. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/323771bdd36.svg.

(1.4.1.3.2.1.21.2.4.2.2.2) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.3.2.1.21.2.4.2.2.2.1) Figure 765. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/323e106d77.svg.

(1.4.1.3.2.1.21.2.4.2.2.2.1) Figure 766. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3236137a25b.svg.

(1.4.1.3.2.1.21.2.4.2.2.2.1) Figure 767. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3235f24fec9.svg.

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